Methods for In Silico Biology: Model Construction and Analysis

Author(s):  
Theresa Yuraszeck ◽  
Peter Chang ◽  
Kalyan Gayen ◽  
Eric Kwei ◽  
Henry Mirsky ◽  
...  
Author(s):  
ICHIRO YAMATO ◽  
TADASHI ANDO ◽  
AYUMI SUZUKI ◽  
KAZUO HARADA ◽  
SEIGO ITOH ◽  
...  
Keyword(s):  

Author(s):  
L. Geris ◽  
J. Vander Sloten ◽  
H. Van Oosterwyck

Bone regeneration is the process whereby bone is able to (scarlessly) repair itself from trauma, such as fractures or implant placement. Despite extensive experimental research, many of the mechanisms involved still remain to be elucidated. Over the last decade, many mathematical models have been established to investigate the regeneration process in silico . The first models considered only the influence of the mechanical environment as a regulator of the healing process. These models were followed by the development of bioregulatory models where mechanics was neglected and regeneration was regulated only by biological stimuli such as growth factors. The most recent mathematical models couple the influences of both biological and mechanical stimuli. Examples are given to illustrate the added value of mathematical regeneration research, specifically in the in silico design of treatment strategies for non-unions. Drawbacks of the current continuum-type models, together with possible solutions in extending the models towards other time and length scales are discussed. Finally, the demands for dedicated and more quantitative experimental research are presented.


2006 ◽  
Vol 25 (3) ◽  
pp. 281-288 ◽  
Author(s):  
Charles Salahuddin
Keyword(s):  

Author(s):  
Md Emran ◽  
Md. Mofijur Rahman ◽  
Afroza Khanam Anika ◽  
Sultana Hossain Nasrin ◽  
Abu Tayab Moin

Tuberculosis (TB) is a contagious disease, caused by Mycobacterium tuberculosis (MTB) that has infected and killed a lot of people in the past. At present treatments against TB are available at a very low cost. Since these chemical drugs have many adverse effects on health, more attention is now given on the plant-derived phytochemicals as potential agents to fight against TB. In this study, 5 phytochemicals, 4-hydroxybenzaldehyde, benzoic acid, bergapten, psoralen, and p-hydroxybenzoic acid, are selected to test their potentiality, safety, and efficacy against two potential targets, the MTB RNA polymerase and enoyl-acyl carrier protein (ACP) reductase, the InhA protein, using various tools of in silico biology. The molecular docking experiment, drug-likeness property test, ADME/T-test, P450 SOM prediction, pharmacophore mapping, and modeling, solubility testing, DFT calculations, and PASS prediction study had confirmed that all the molecules had the good potentiality to inhibit the two targets. However, two agents, 4-hydroxybenzaldehyde and bergapten were considered as the best agents among the five selected agents and they also showed far better results than the two currently used drugs, that function in these pathways, rifampicin (MTB RNA polymerase) and isoniazid (InhA protein). These two agents can be used effectively to treat tuberculosis.


BIOSILICO ◽  
2003 ◽  
Vol 1 (1) ◽  
pp. 18-22 ◽  
Author(s):  
Alex L. Bangs ◽  
Thomas S. Paterson
Keyword(s):  

10.1038/81125 ◽  
2000 ◽  
Vol 18 (11) ◽  
pp. 1147-1150 ◽  
Author(s):  
Bernhard Palsson
Keyword(s):  

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